You have been already told to use %ENV to work with these variables. Try something like this:

if (fork == 0) {
 # create a subprocess
 $ENV{myvariablename} = "desired variable value";
 # set the variable
 ...
 exec("/path/to/program","some","program","arguments");
 # run the program
}
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If you need to write shell commands, just run a shell and write your shell commands into it:

open my $shell, "|/bin/sh" || die "$!\n";
print $shell "export var=value\n";
...
print $shell "some complicated shell command # ;(){:|:&};:\n";
print $shell "/run/the/program --with-args\n";
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Or use multi-line system(), for example, with here-doc:

system <<"END";
export var=value
...
some() {shell commands}
/run/some/program
END
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